1
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Roth GV, Gengaro IR, Qi LS. Precision epigenetic editing: Technological advances, enduring challenges, and therapeutic applications. Cell Chem Biol 2024:S2451-9456(24)00309-X. [PMID: 39137782 DOI: 10.1016/j.chembiol.2024.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/31/2024] [Accepted: 07/15/2024] [Indexed: 08/15/2024]
Abstract
The epigenome is a complex framework through which gene expression is precisely and flexibly modulated to incorporate heritable memory and responses to environmental stimuli. It governs diverse cellular processes, including cell fate, disease, and aging. The need to understand this system and precisely control gene expression outputs for therapeutic purposes has precipitated the development of a diverse set of epigenetic editing tools. Here, we review the existing toolbox for targeted epigenetic editing, technical considerations of the current technologies, and opportunities for future development. We describe applications of therapeutic epigenetic editing and their potential for treating disease, with a discussion of ongoing delivery challenges that impede certain clinical interventions, particularly in the brain. With simultaneous advancements in available engineering tools and appropriate delivery technologies, we predict that epigenetic editing will increasingly cement itself as a powerful approach for safely treating a wide range of disorders in all tissues of the body.
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Affiliation(s)
- Goldie V Roth
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
| | - Isabella R Gengaro
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA; Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Lei S Qi
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA; Department of Bioengineering, Stanford University, Stanford, CA, USA; Chan Zuckerberg Biohub - San Francisco, San Francisco, CA, USA.
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2
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Wang L, Bai Y, Cao Z, Guo Z, Lian Y, Liu P, Zeng Y, Lyu W, Chen Q. Histone deacetylases and inhibitors in diabetes mellitus and its complications. Biomed Pharmacother 2024; 177:117010. [PMID: 38941890 DOI: 10.1016/j.biopha.2024.117010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/29/2024] [Accepted: 06/17/2024] [Indexed: 06/30/2024] Open
Abstract
Diabetes mellitus (DM) is a metabolic disorder characterized by hyperglycemia, with its prevalence linked to both genetic predisposition and environmental factors. Epigenetic modifications, particularly through histone deacetylases (HDACs), have been recognized for their significant influence on DM pathogenesis. This review focuses on the classification of HDACs, their role in DM and its complications, and the potential therapeutic applications of HDAC inhibitors. HDACs, which modulate gene expression without altering DNA sequences, are categorized into four classes with distinct functions and tissue specificity. HDAC inhibitors (HDACi) have shown efficacy in various diseases, including DM, by targeting these enzymes. The review highlights how HDACs regulate β-cell function, insulin sensitivity, and hepatic gluconeogenesis in DM, as well as their impact on diabetic cardiomyopathy, nephropathy, and retinopathy. Finally, we suggest that targeted histone modification is expected to become a key method for the treatment of diabetes and its complications. The study of HDACi offers insights into new treatment strategies for DM and its associated complications.
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Affiliation(s)
- Li Wang
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan Province 610072, PR China; Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing 100053, PR China
| | - Yuning Bai
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing 100053, PR China
| | - Zhengmin Cao
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing 100053, PR China
| | - Ziwei Guo
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing 100053, PR China
| | - Yanjie Lian
- Department of Cardiovascular Medicine, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing 100010, PR China
| | - Pan Liu
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan Province 610072, PR China
| | - Yixian Zeng
- Department of Proctology, Beibei Hospital of Traditional Chinese Medicine, Chongqing 400799, PR China
| | - Wenliang Lyu
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing 100053, PR China.
| | - Qiu Chen
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan Province 610072, PR China.
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3
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Liang Y, Carrillo-Baltodano AM, Martín-Durán JM. Emerging trends in the study of spiralian larvae. Evol Dev 2024; 26:e12459. [PMID: 37787615 DOI: 10.1111/ede.12459] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 09/11/2023] [Accepted: 09/13/2023] [Indexed: 10/04/2023]
Abstract
Many animals undergo indirect development, where their embryogenesis produces an intermediate life stage, or larva, that is often free-living and later metamorphoses into an adult. As their adult counterparts, larvae can have unique and diverse morphologies and occupy various ecological niches. Given their broad phylogenetic distribution, larvae have been central to hypotheses about animal evolution. However, the evolution of these intermediate forms and the developmental mechanisms diversifying animal life cycles are still debated. This review focuses on Spiralia, a large and diverse clade of bilaterally symmetrical animals with a fascinating array of larval forms, most notably the archetypical trochophore larva. We explore how classic research and modern advances have improved our understanding of spiralian larvae, their development, and evolution. Specifically, we examine three morphological features of spiralian larvae: the anterior neural system, the ciliary bands, and the posterior hyposphere. The combination of molecular and developmental evidence with modern high-throughput techniques, such as comparative genomics, single-cell transcriptomics, and epigenomics, is a promising strategy that will lead to new testable hypotheses about the mechanisms behind the evolution of larvae and life cycles in Spiralia and animals in general. We predict that the increasing number of available genomes for Spiralia and the optimization of genome-wide and single-cell approaches will unlock the study of many emerging spiralian taxa, transforming our views of the evolution of this animal group and their larvae.
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Affiliation(s)
- Yan Liang
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | | | - José M Martín-Durán
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
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4
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Bedi K, Magnuson B, Narayanan IV, McShane A, Ashaka M, Paulsen MT, Wilson TE, Ljungman M. Isoform and pathway-specific regulation of post-transcriptional RNA processing in human cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.12.598705. [PMID: 38915566 PMCID: PMC11195214 DOI: 10.1101/2024.06.12.598705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Steady-state levels of RNA transcripts are controlled by their rates of synthesis and degradation. Here we used nascent RNA Bru-seq and BruChase-seq to profile RNA dynamics across 16 human cell lines as part of ENCODE4 Deeply Profiled Cell Lines collection. We show that RNA turnover dynamics differ widely between transcripts of different genes and between different classes of RNA. Gene set enrichment analysis (GSEA) revealed that transcripts encoding proteins belonging to the same pathway often show similar turnover dynamics. Furthermore, transcript isoforms show distinct dynamics suggesting that RNA turnover is important in regulating mRNA isoform choice. Finally, splicing across newly made transcripts appears to be cooperative with either all or none type splicing. These data sets generated as part of ENCODE4 illustrate the intricate and coordinated regulation of RNA dynamics in controlling gene expression to allow for the precise coordination of cellular functions.
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Affiliation(s)
- Karan Bedi
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Brian Magnuson
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Pathology and Department of Human Genetics, University of Michigan Medical School, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Ariel McShane
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mario Ashaka
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michelle T Paulsen
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Thomas E Wilson
- Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Pathology and Department of Human Genetics, University of Michigan Medical School, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
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5
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Pepke ML, Hansen SB, Limborg MT. Unraveling host regulation of gut microbiota through the epigenome-microbiome axis. Trends Microbiol 2024:S0966-842X(24)00137-9. [PMID: 38839511 DOI: 10.1016/j.tim.2024.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 05/13/2024] [Accepted: 05/15/2024] [Indexed: 06/07/2024]
Abstract
Recent studies of dynamic interactions between epigenetic modifications of a host organism and the composition or activity of its associated gut microbiota suggest an opportunity for the host to shape its microbiome through epigenetic alterations that lead to changes in gene expression and noncoding RNA activity. We use insights from microbiota-induced epigenetic changes to review the potential of the host to epigenetically regulate its gut microbiome, from which a bidirectional 'epigenome-microbiome axis' emerges. This axis embeds environmentally induced variation, which may influence the adaptive evolution of host-microbe interactions. We furthermore present our perspective on how the epigenome-microbiome axis can be understood and investigated within a holo-omic framework with potential applications in the applied health and food sciences.
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Affiliation(s)
- Michael L Pepke
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5, DK-1353 Copenhagen, Denmark.
| | - Søren B Hansen
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5, DK-1353 Copenhagen, Denmark
| | - Morten T Limborg
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5, DK-1353 Copenhagen, Denmark.
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6
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Policarpi C, Munafò M, Tsagkris S, Carlini V, Hackett JA. Systematic epigenome editing captures the context-dependent instructive function of chromatin modifications. Nat Genet 2024; 56:1168-1180. [PMID: 38724747 PMCID: PMC11176084 DOI: 10.1038/s41588-024-01706-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 03/05/2024] [Indexed: 05/22/2024]
Abstract
Chromatin modifications are linked with regulating patterns of gene expression, but their causal role and context-dependent impact on transcription remains unresolved. Here we develop a modular epigenome editing platform that programs nine key chromatin modifications, or combinations thereof, to precise loci in living cells. We couple this with single-cell readouts to systematically quantitate the magnitude and heterogeneity of transcriptional responses elicited by each specific chromatin modification. Among these, we show that installing histone H3 lysine 4 trimethylation (H3K4me3) at promoters can causally instruct transcription by hierarchically remodeling the chromatin landscape. We further dissect how DNA sequence motifs influence the transcriptional impact of chromatin marks, identifying switch-like and attenuative effects within distinct cis contexts. Finally, we examine the interplay of combinatorial modifications, revealing that co-targeted H3K27 trimethylation (H3K27me3) and H2AK119 monoubiquitination (H2AK119ub) maximizes silencing penetrance across single cells. Our precision-perturbation strategy unveils the causal principles of how chromatin modification(s) influence transcription and dissects how quantitative responses are calibrated by contextual interactions.
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Affiliation(s)
- Cristina Policarpi
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Rome, Italy
| | - Marzia Munafò
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Rome, Italy
| | - Stylianos Tsagkris
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Rome, Italy
| | - Valentina Carlini
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Rome, Italy
- Faculty of Biosciences, EMBL and Heidelberg University, Heidelberg, Germany
| | - Jamie A Hackett
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Rome, Italy.
- Genome Biology Unit, EMBL, Heidelberg, Germany.
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7
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Chromatin modifications integrate cis genomic context to instruct transcriptional outputs. Nat Genet 2024; 56:1051-1052. [PMID: 38769458 DOI: 10.1038/s41588-024-01705-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
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8
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Bell CG. Epigenomic insights into common human disease pathology. Cell Mol Life Sci 2024; 81:178. [PMID: 38602535 PMCID: PMC11008083 DOI: 10.1007/s00018-024-05206-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 04/12/2024]
Abstract
The epigenome-the chemical modifications and chromatin-related packaging of the genome-enables the same genetic template to be activated or repressed in different cellular settings. This multi-layered mechanism facilitates cell-type specific function by setting the local sequence and 3D interactive activity level. Gene transcription is further modulated through the interplay with transcription factors and co-regulators. The human body requires this epigenomic apparatus to be precisely installed throughout development and then adequately maintained during the lifespan. The causal role of the epigenome in human pathology, beyond imprinting disorders and specific tumour suppressor genes, was further brought into the spotlight by large-scale sequencing projects identifying that mutations in epigenomic machinery genes could be critical drivers in both cancer and developmental disorders. Abrogation of this cellular mechanism is providing new molecular insights into pathogenesis. However, deciphering the full breadth and implications of these epigenomic changes remains challenging. Knowledge is accruing regarding disease mechanisms and clinical biomarkers, through pathogenically relevant and surrogate tissue analyses, respectively. Advances include consortia generated cell-type specific reference epigenomes, high-throughput DNA methylome association studies, as well as insights into ageing-related diseases from biological 'clocks' constructed by machine learning algorithms. Also, 3rd-generation sequencing is beginning to disentangle the complexity of genetic and DNA modification haplotypes. Cell-free DNA methylation as a cancer biomarker has clear clinical utility and further potential to assess organ damage across many disorders. Finally, molecular understanding of disease aetiology brings with it the opportunity for exact therapeutic alteration of the epigenome through CRISPR-activation or inhibition.
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Affiliation(s)
- Christopher G Bell
- William Harvey Research Institute, Barts & The London Faculty of Medicine, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK.
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Stricker SH, Pereira CF. Reprogramming Stars #15: Colliding Cellular Reprogramming Paths- An Interview with Dr. Stefan Stricker. Cell Reprogram 2024; 26:37-42. [PMID: 38635923 DOI: 10.1089/cell.2024.29115.shs] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024] Open
Affiliation(s)
- Stefan H Stricker
- Reprogramming and Regeneration, Biomedical Center (BMC), Physiological Genomics, Faculty of Medicine, LMU Munich. Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, Planegg-Martinsried, Germany
| | - Carlos-Filipe Pereira
- Molecular Medicine and Gene Therapy, Lund Stem Cell Centre, Wallenberg Centre for Molecular Medicine, Lund University, Lund, Sweden
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Xu G, Law JA. Loops, crosstalk, and compartmentalization: it takes many layers to regulate DNA methylation. Curr Opin Genet Dev 2024; 84:102147. [PMID: 38176333 PMCID: PMC10922829 DOI: 10.1016/j.gde.2023.102147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 12/06/2023] [Accepted: 12/06/2023] [Indexed: 01/06/2024]
Abstract
DNA methylation is a conserved epigenetic modification associated with transposon silencing and gene regulation. The stability of this modification relies on intimate connections between DNA and histone modifications that generate self-reinforcing loops wherein the presence of one mark promotes the other. However, it is becoming increasingly clear that the efficiency of these loops is affected by cross-talk between pathways and by chromatin accessibility, which is heavily influenced by histone variants. Focusing primarily on plants, this review provides an update on the aforementioned self-reinforcing loops, highlights recent advances in understanding how DNA methylation pathways are restricted to prevent encroachment on genes, and discusses the roles of histone variants in compartmentalizing epigenetic pathways within the genome. This multilayered approach facilitates two essential, yet opposing functions, the ability to maintain heritable DNA methylation patterns while retaining the flexibility to modify these patterns during development.
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Affiliation(s)
- Guanghui Xu
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA. https://twitter.com/@GuanghuiXu1
| | - Julie A Law
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
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Chen Y, Yang S, Yu K, Zhang J, Wu M, Zheng Y, Zhu Y, Dai J, Wang C, Zhu X, Dai Y, Sun Y, Wu T, Wang S. Spatial omics: An innovative frontier in aging research. Ageing Res Rev 2024; 93:102158. [PMID: 38056503 DOI: 10.1016/j.arr.2023.102158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/25/2023] [Accepted: 12/01/2023] [Indexed: 12/08/2023]
Abstract
Disentangling the impact of aging on health and disease has become critical as population aging progresses rapidly. Studying aging at the molecular level is complicated by the diverse aging profiles and dynamics. However, the examination of cellular states within aging tissues in situ is hampered by the lack of high-resolution spatial data. Emerging spatial omics technologies facilitate molecular and spatial analysis of tissues, providing direct access to precise information on various functional regions and serving as a favorable tool for unraveling the heterogeneity of aging. In this review, we summarize the recent advances in spatial omics application in multi-organ aging research, which has enhanced the understanding of aging mechanisms from multiple standpoints. We also discuss the main challenges in spatial omics research to date, the opportunities for further developing the technology, and the potential applications of spatial omics in aging and aging-related diseases.
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Affiliation(s)
- Ying Chen
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China; Ministry of Education, Key Laboratory of Cancer Invasion and Metastasis, Wuhan, China
| | - Shuhao Yang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China; Ministry of Education, Key Laboratory of Cancer Invasion and Metastasis, Wuhan, China
| | - Kaixu Yu
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jinjin Zhang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China; Ministry of Education, Key Laboratory of Cancer Invasion and Metastasis, Wuhan, China
| | - Meng Wu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China; Ministry of Education, Key Laboratory of Cancer Invasion and Metastasis, Wuhan, China
| | - Yongqiang Zheng
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Centre, Sun Yat-sen University, Guangzhou, China
| | - Yun Zhu
- Department of Internal Medicine, Southern Illinois University School of Medicine, 801 N. Rutledge, P.O. Box 19628, Springfield, IL 62702, USA
| | - Jun Dai
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China; Ministry of Education, Key Laboratory of Cancer Invasion and Metastasis, Wuhan, China
| | - Chunyan Wang
- College of Science & Engineering Jinan University, Guangzhou, China
| | - Xiaoran Zhu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China; Ministry of Education, Key Laboratory of Cancer Invasion and Metastasis, Wuhan, China
| | - Yun Dai
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China; Ministry of Education, Key Laboratory of Cancer Invasion and Metastasis, Wuhan, China
| | - Yunhong Sun
- Hubei Key Laboratory of Food Nutrition and Safety, MOE Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tong Wu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China; Ministry of Education, Key Laboratory of Cancer Invasion and Metastasis, Wuhan, China.
| | - Shixuan Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrical and Gynecological Diseases, Wuhan, China; Ministry of Education, Key Laboratory of Cancer Invasion and Metastasis, Wuhan, China.
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12
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Wang W, Li H, Shi Y, Zhou J, Khan GJ, Zhu J, Liu F, Duan H, Li L, Zhai K. Targeted intervention of natural medicinal active ingredients and traditional Chinese medicine on epigenetic modification: Possible strategies for prevention and treatment of atherosclerosis. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 122:155139. [PMID: 37863003 DOI: 10.1016/j.phymed.2023.155139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 09/26/2023] [Accepted: 10/05/2023] [Indexed: 10/22/2023]
Abstract
BACKGROUND Atherosclerosis is a deadly consequence of cardiovascular disease and has very high mortality rate worldwide. The epigenetic modifications can regulate the pervasiveness and progression of atherosclerosis through its involvement in regulation of inflammation, oxidative stress, lipid metabolism and several other factors. Specific non-coding RNAs, DNA methylation, and histone modifications are key regulatory factors of atherosclerosis. Natural products from traditional Chinese medicine have shown promising therapeutic potential against atherosclerosis by means of regulating the expression of specific genes, stabilizing arterial plaques and protecting vascular endothelial cells. OBJECTIVE Our study is focusing to explore the pathophysiology and probability of traditional Chinese medicine and natural medicinal active ingredients to treat atherosclerosis. METHODS Comprehensive literature review was conducted using PubMed, Web of Science, Google Scholar and China National Knowledge Infrastructure with a core focus on natural medicinal active ingredients and traditional Chinese medicine prying in epigenetic modification related to atherosclerosis. RESULTS Accumulated evidence demonstrated that natural medicinal active ingredients and traditional Chinese medicine have been widely studied as substances that can regulate epigenetic modification. They can participate in the occurrence and development of atherosclerosis through inflammation, oxidative stress, lipid metabolism, cell proliferation and migration, macrophage polarization and autophagy respectively. CONCLUSION The function of natural medicinal active ingredients and traditional Chinese medicine in regulating epigenetic modification may provide a new potential strategy for the prevention and treatment of atherosclerosis. However, more extensive research is essential to determine the potential of these natural medicinal active ingredients to treat atherosclerosis because of least clinical data.
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Affiliation(s)
- Wei Wang
- School of Biological and Food Engineering, Engineering Research Center for Development and High Value Utilization of Genuine Medicinal Materials in North Anhui Province, Suzhou University, Suzhou, Anhui 234000, China; College of Biological and Food Engineering, Anhui Polytechnic University, Wuhu, Anhui 241000, China
| | - Han Li
- School of Biological and Food Engineering, Engineering Research Center for Development and High Value Utilization of Genuine Medicinal Materials in North Anhui Province, Suzhou University, Suzhou, Anhui 234000, China; College of Biological and Food Engineering, Anhui Polytechnic University, Wuhu, Anhui 241000, China
| | - Ying Shi
- School of Biological and Food Engineering, Engineering Research Center for Development and High Value Utilization of Genuine Medicinal Materials in North Anhui Province, Suzhou University, Suzhou, Anhui 234000, China; College of Biological and Food Engineering, Anhui Polytechnic University, Wuhu, Anhui 241000, China
| | - Jing Zhou
- School of Biological and Food Engineering, Engineering Research Center for Development and High Value Utilization of Genuine Medicinal Materials in North Anhui Province, Suzhou University, Suzhou, Anhui 234000, China; College of Biological and Food Engineering, Anhui Polytechnic University, Wuhu, Anhui 241000, China
| | - Ghulam Jilany Khan
- Department of Pharmacology and Therapeutics, Faculty of Pharmacy, University of Central Punjab, Lahore 54000, Pakistan
| | - Juan Zhu
- School of Biological and Food Engineering, Engineering Research Center for Development and High Value Utilization of Genuine Medicinal Materials in North Anhui Province, Suzhou University, Suzhou, Anhui 234000, China; Faculty of Pharmacy, Bengbu Medical College, Bengbu, Anhui 233030, China
| | - Fawang Liu
- School of Biological and Food Engineering, Engineering Research Center for Development and High Value Utilization of Genuine Medicinal Materials in North Anhui Province, Suzhou University, Suzhou, Anhui 234000, China; Anhui Province Key Laboratory of Research & Development of Chinese Medicine, Hefei, Anhui 230012, China
| | - Hong Duan
- School of Biological and Food Engineering, Engineering Research Center for Development and High Value Utilization of Genuine Medicinal Materials in North Anhui Province, Suzhou University, Suzhou, Anhui 234000, China; College of Biological and Food Engineering, Anhui Polytechnic University, Wuhu, Anhui 241000, China.
| | - Lili Li
- General Clinical Research Center, Anhui Wanbei Coal-Electricity Group General Hospital, Suzhou 234000, China.
| | - Kefeng Zhai
- School of Biological and Food Engineering, Engineering Research Center for Development and High Value Utilization of Genuine Medicinal Materials in North Anhui Province, Suzhou University, Suzhou, Anhui 234000, China; College of Biological and Food Engineering, Anhui Polytechnic University, Wuhu, Anhui 241000, China; Faculty of Pharmacy, Bengbu Medical College, Bengbu, Anhui 233030, China.
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13
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Jin W, Yan W, Ma M, Hasi A, Che G. Genome-wide identification and expression analysis of the JMJ-C gene family in melon (Cucumis melo L.) reveals their potential role in fruit development. BMC Genomics 2023; 24:771. [PMID: 38093236 PMCID: PMC10720240 DOI: 10.1186/s12864-023-09868-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/03/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Proteins with the jumonji (JMJ)-C domain belong to the histone demethylase family and contribute to reverse histone methylation. Although JMJ-C family genes have an essential role in regulating plant growth and development, the characterization of the JMJ-C family genes in melon has not been uncovered. RESULTS In this study, a total of 17 JMJ-C proteins were identified in melon (Cucumis melo L.). CmJMJs were categorized into five subfamilies based on the specific conserved domain: KDM4/JHDM3, KDM5/JARID1, JMJD6, KDM3/JHDM2, and JMJ-C domain-only. The chromosome localization analyses showed that 17 CmJMJs were distributed on nine chromosomes. Cis-acting element analyses of the 17 CmJMJ genes showed numerous hormone, light, and stress response elements distributed in the promoter region. Covariance analysis revealed one pair of replicated fragments (CmJMJ3a and CmJMJ3b) in 17 CmJMJ genes. We investigated the expression profile of 17 CmJMJ genes in different lateral organs and four developmental stages of fruit by RNA-seq transcriptome analysis and RT-qPCR. The results revealed that most CmJMJ genes were prominently expressed in female flowers, ovaries, and developing fruits, suggesting their active role in melon fruit development. Subcellular localization showed that the fruit-related CmJMJ5a protein is specifically localized in the cell nucleus. CONCLUSIONS This study provides a comprehensive understanding of the gene structure, classification, and evolution of JMJ-C in melon and supports the clarification of the JMJ-C functions in further research.
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Affiliation(s)
- Wuyun Jin
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Wei Yan
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Ming Ma
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Agula Hasi
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
| | - Gen Che
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
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14
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Fu Q, Frick JM, O'Neil MF, Eller OC, Morris EM, Thyfault JP, Christianson JA, Lane RH. Early-life stress perturbs the epigenetics of Cd36 concurrent with adult onset of NAFLD in mice. Pediatr Res 2023; 94:1942-1950. [PMID: 37479748 PMCID: PMC10665193 DOI: 10.1038/s41390-023-02714-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 05/03/2023] [Accepted: 06/15/2023] [Indexed: 07/23/2023]
Abstract
BACKGROUND Non-alcoholic fatty liver disease (NAFLD) is one of the most common liver diseases in the U.S. and worldwide. The roles of early postnatal life stress (EPLS) and the fatty acid translocase (CD36) on the pathogenesis of adult-onset NAFLD remain unknown. We hypothesized that EPLS, in the form of neonatal maternal separation (NMS), would predispose mice towards developing adult NAFLD, increase hepatic CD36 expression, and differentially methylate Cd36 promoter concurrently. METHODS NMS was performed on mice from postnatal day 1 to 21 and a high-fat/high-sucrose (HFS) diet was started at 4 weeks of age to generate four experimental groups: Naive-control diet (CD), Naive-HFS, NMS-CD, and NMS-HFS. RESULTS NMS alone caused NAFLD in adult male mice at 25 weeks of age. The effects of NMS and HFS were generally additive in terms of NAFLD, hepatic Cd36 mRNA levels, and hepatic Cd36 promoter DNA hypomethylation. Cd36 promoter methylation negatively correlated with Cd36 mRNA levels. Two differentially methylated regions (DMRs) within Cd36 promoter regions appeared to be vulnerable to NMS in the mouse. CONCLUSIONS Our findings suggest that NMS increases the risk of an individual, particularly male, towards NAFLD when faced with a HFS diet later in life. IMPACT The key message of this article is that neonatal maternal separation and a postweaning high-fat/high-sucrose diet increased the risk of an individual, particularly male, towards NAFLD in adult life. What this study adds to the existing literature includes the identification of two vulnerable differentially methylated regions in hepatic Cd36 promoters whose methylation levels very strongly negatively correlated with Cd36 mRNA. The impact of this article is that it provides an early-life environment-responsive gene/promoter methylation model and an animal model for furthering the mechanistic study on how the insults in early-life environment are "transmitted" into adulthood and caused NAFLD.
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Affiliation(s)
- Qi Fu
- Department of Research Administration, Children's Mercy Hospital, Kansas City, MO, USA
| | - Jenna M Frick
- Department of Anatomy and Cell Biology, School of Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Maura F O'Neil
- Department of Pathology and Laboratory Medicine, School of Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Olivia C Eller
- Department of Anatomy and Cell Biology, School of Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - E Matthew Morris
- Department of Molecular and Integrative Physiology, School of Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - John P Thyfault
- Department of Molecular and Integrative Physiology, School of Medicine, University of Kansas Medical Center, Kansas City, KS, USA
- Research Service, Kansas City VA Medical Center, Kansas City, KS, USA
| | - Julie A Christianson
- Department of Anatomy and Cell Biology, School of Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Robert H Lane
- Department of Administration, Children's Mercy Hospital, Kansas City, MO, USA.
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15
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Heuts BMH, Martens JHA. Understanding blood development and leukemia using sequencing-based technologies and human cell systems. Front Mol Biosci 2023; 10:1266697. [PMID: 37886034 PMCID: PMC10598665 DOI: 10.3389/fmolb.2023.1266697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 09/06/2023] [Indexed: 10/28/2023] Open
Abstract
Our current understanding of human hematopoiesis has undergone significant transformation throughout the years, challenging conventional views. The evolution of high-throughput technologies has enabled the accumulation of diverse data types, offering new avenues for investigating key regulatory processes in blood cell production and disease. In this review, we will explore the opportunities presented by these advancements for unraveling the molecular mechanisms underlying normal and abnormal hematopoiesis. Specifically, we will focus on the importance of enhancer-associated regulatory networks and highlight the crucial role of enhancer-derived transcription regulation. Additionally, we will discuss the unprecedented power of single-cell methods and the progression in using in vitro human blood differentiation system, in particular induced pluripotent stem cell models, in dissecting hematopoietic processes. Furthermore, we will explore the potential of ever more nuanced patient profiling to allow precision medicine approaches. Ultimately, we advocate for a multiparameter, regulatory network-based approach for providing a more holistic understanding of normal hematopoiesis and blood disorders.
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Affiliation(s)
- Branco M H Heuts
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen, Netherlands
| | - Joost H A Martens
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen, Netherlands
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16
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Batra SS, Cabrera A, Spence JP, Hilton IB, Song YS. Predicting the effect of CRISPR-Cas9-based epigenome editing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.03.560674. [PMID: 37873127 PMCID: PMC10592942 DOI: 10.1101/2023.10.03.560674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Epigenetic regulation orchestrates mammalian transcription, but functional links between them remain elusive. To tackle this problem, we here use epigenomic and transcriptomic data from 13 ENCODE cell types to train machine learning models to predict gene expression from histone post-translational modifications (PTMs), achieving transcriptome-wide correlations of ~ 0.70 - 0.79 for most samples. In addition to recapitulating known associations between histone PTMs and expression patterns, our models predict that acetylation of histone subunit H3 lysine residue 27 (H3K27ac) near the transcription start site (TSS) significantly increases expression levels. To validate this prediction experimentally and investigate how engineered vs. natural deposition of H3K27ac might differentially affect expression, we apply the synthetic dCas9-p300 histone acetyltransferase system to 8 genes in the HEK293T cell line. Further, to facilitate model building, we perform MNase-seq to map genome-wide nucleosome occupancy levels in HEK293T. We observe that our models perform well in accurately ranking relative fold changes among genes in response to the dCas9-p300 system; however, their ability to rank fold changes within individual genes is noticeably diminished compared to predicting expression across cell types from their native epigenetic signatures. Our findings highlight the need for more comprehensive genome-scale epigenome editing datasets, better understanding of the actual modifications made by epigenome editing tools, and improved causal models that transfer better from endogenous cellular measurements to perturbation experiments. Together these improvements would facilitate the ability to understand and predictably control the dynamic human epigenome with consequences for human health.
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Affiliation(s)
| | | | | | - Isaac B. Hilton
- Department of Bioengineering, Rice University
- Department of BioSciences, Rice University
| | - Yun S. Song
- Computer Science Division, University of California, Berkeley
- Department of Statistics, University of California, Berkeley
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17
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Liu C, Wang Z, Wang J, Liu C, Wang M, Ngo V, Wang W. Predicting regional somatic mutation rates using DNA motifs. PLoS Comput Biol 2023; 19:e1011536. [PMID: 37782656 PMCID: PMC10569533 DOI: 10.1371/journal.pcbi.1011536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 10/12/2023] [Accepted: 09/20/2023] [Indexed: 10/04/2023] Open
Abstract
How the locus-specificity of epigenetic modifications is regulated remains an unanswered question. A contributing mechanism is that epigenetic enzymes are recruited to specific loci by DNA binding factors recognizing particular sequence motifs (referred to as epi-motifs). Using these motifs to predict biological outputs depending on local epigenetic state such as somatic mutation rates would confirm their functionality. Here, we used DNA motifs including known TF motifs and epi-motifs as a surrogate of epigenetic signals to predict somatic mutation rates in 13 cancers at an average 23kbp resolution. We implemented an interpretable neural network model, called contextual regression, to successfully learn the universal relationship between mutations and DNA motifs, and uncovered motifs that are most impactful on the regional mutation rates such as TP53 and epi-motifs associated with H3K9me3. Furthermore, we identified genomic regions with significantly higher mutation rates than the expected values in each individual tumor and demonstrated that such cancer-related regions can accurately predict cancer types. Interestingly, we found that the same mutation signatures often have different contributions to cancer-related and cancer-independent regions, and we also identified the motifs with the most contribution to each mutation signature.
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Affiliation(s)
- Cong Liu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Zengmiao Wang
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Jun Wang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Chengyu Liu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Mengchi Wang
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, California, United States of America
| | - Vu Ngo
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, California, United States of America
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, California, United States of America
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, United States of America
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18
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Dai Y, Ren D, He Y, Yi H. Editorial: Epigenetic, metabolic, and transcriptional regulation of immune cell plasticity and functions in cancer and non-cancer diseases. Front Immunol 2023; 14:1284124. [PMID: 37818355 PMCID: PMC10561278 DOI: 10.3389/fimmu.2023.1284124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 09/18/2023] [Indexed: 10/12/2023] Open
Affiliation(s)
- Yun Dai
- Laboratory of Cancer Precision Medicine, the First Hospital of Jilin University, Changchun, Jilin, China
| | - Dong Ren
- Irvine Medical Center, University of California, Irvine, Irvine, CA, United States
| | - Yafeng He
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Huanfa Yi
- Central Laboratory, the First Hospital of Jilin University, Changchun, Jilin, China
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19
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Chen C, Wang J, Pan D, Wang X, Xu Y, Yan J, Wang L, Yang X, Yang M, Liu G. Applications of multi-omics analysis in human diseases. MedComm (Beijing) 2023; 4:e315. [PMID: 37533767 PMCID: PMC10390758 DOI: 10.1002/mco2.315] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/25/2023] [Accepted: 05/31/2023] [Indexed: 08/04/2023] Open
Abstract
Multi-omics usually refers to the crossover application of multiple high-throughput screening technologies represented by genomics, transcriptomics, single-cell transcriptomics, proteomics and metabolomics, spatial transcriptomics, and so on, which play a great role in promoting the study of human diseases. Most of the current reviews focus on describing the development of multi-omics technologies, data integration, and application to a particular disease; however, few of them provide a comprehensive and systematic introduction of multi-omics. This review outlines the existing technical categories of multi-omics, cautions for experimental design, focuses on the integrated analysis methods of multi-omics, especially the approach of machine learning and deep learning in multi-omics data integration and the corresponding tools, and the application of multi-omics in medical researches (e.g., cancer, neurodegenerative diseases, aging, and drug target discovery) as well as the corresponding open-source analysis tools and databases, and finally, discusses the challenges and future directions of multi-omics integration and application in precision medicine. With the development of high-throughput technologies and data integration algorithms, as important directions of multi-omics for future disease research, single-cell multi-omics and spatial multi-omics also provided a detailed introduction. This review will provide important guidance for researchers, especially who are just entering into multi-omics medical research.
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Affiliation(s)
- Chongyang Chen
- Key Laboratory of Nuclear MedicineMinistry of HealthJiangsu Key Laboratory of Molecular Nuclear MedicineJiangsu Institute of Nuclear MedicineWuxiChina
- Co‐innovation Center of NeurodegenerationNantong UniversityNantongChina
| | - Jing Wang
- Shenzhen Key Laboratory of Modern ToxicologyShenzhen Medical Key Discipline of Health Toxicology (2020–2024)Shenzhen Center for Disease Control and PreventionShenzhenChina
| | - Donghui Pan
- Key Laboratory of Nuclear MedicineMinistry of HealthJiangsu Key Laboratory of Molecular Nuclear MedicineJiangsu Institute of Nuclear MedicineWuxiChina
| | - Xinyu Wang
- Key Laboratory of Nuclear MedicineMinistry of HealthJiangsu Key Laboratory of Molecular Nuclear MedicineJiangsu Institute of Nuclear MedicineWuxiChina
| | - Yuping Xu
- Key Laboratory of Nuclear MedicineMinistry of HealthJiangsu Key Laboratory of Molecular Nuclear MedicineJiangsu Institute of Nuclear MedicineWuxiChina
| | - Junjie Yan
- Key Laboratory of Nuclear MedicineMinistry of HealthJiangsu Key Laboratory of Molecular Nuclear MedicineJiangsu Institute of Nuclear MedicineWuxiChina
| | - Lizhen Wang
- Key Laboratory of Nuclear MedicineMinistry of HealthJiangsu Key Laboratory of Molecular Nuclear MedicineJiangsu Institute of Nuclear MedicineWuxiChina
| | - Xifei Yang
- Shenzhen Key Laboratory of Modern ToxicologyShenzhen Medical Key Discipline of Health Toxicology (2020–2024)Shenzhen Center for Disease Control and PreventionShenzhenChina
| | - Min Yang
- Key Laboratory of Nuclear MedicineMinistry of HealthJiangsu Key Laboratory of Molecular Nuclear MedicineJiangsu Institute of Nuclear MedicineWuxiChina
| | - Gong‐Ping Liu
- Co‐innovation Center of NeurodegenerationNantong UniversityNantongChina
- Department of PathophysiologySchool of Basic MedicineKey Laboratory of Ministry of Education of China and Hubei Province for Neurological DisordersTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
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20
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Sakaguchi S, Mizuno S, Okochi Y, Tanegashima C, Nishimura O, Uemura T, Kadota M, Naoki H, Kondo T. Single-cell transcriptome atlas of Drosophila gastrula 2.0. Cell Rep 2023:112707. [PMID: 37433294 DOI: 10.1016/j.celrep.2023.112707] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/27/2023] [Accepted: 06/13/2023] [Indexed: 07/13/2023] Open
Abstract
During development, positional information directs cells to specific fates, leading them to differentiate with their own transcriptomes and express specific behaviors and functions. However, the mechanisms underlying these processes in a genome-wide view remain ambiguous, partly because the single-cell transcriptomic data of early developing embryos containing accurate spatial and lineage information are still lacking. Here, we report a single-cell transcriptome atlas of Drosophila gastrulae, divided into 77 transcriptomically distinct clusters. We find that the expression profiles of plasma-membrane-related genes, but not those of transcription-factor genes, represent each germ layer, supporting the nonequivalent contribution of each transcription-factor mRNA level to effector gene expression profiles at the transcriptome level. We also reconstruct the spatial expression patterns of all genes at the single-cell stripe level as the smallest unit. This atlas is an important resource for the genome-wide understanding of the mechanisms by which genes cooperatively orchestrate Drosophila gastrulation.
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Affiliation(s)
- Shunta Sakaguchi
- Laboratory of Cell Recognition and Pattern Formation, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Sonoko Mizuno
- Laboratory of Cell Recognition and Pattern Formation, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yasushi Okochi
- Laboratory of Theoretical Biology, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan; Faculty of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Chiharu Tanegashima
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Osamu Nishimura
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Tadashi Uemura
- Laboratory of Cell Recognition and Pattern Formation, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan; Center for Living Systems Information Science, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Mitsutaka Kadota
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Honda Naoki
- Laboratory of Theoretical Biology, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan; Laboratory of Data-driven Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Hiroshima 739-8511, Japan; Theoretical Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8585, Japan
| | - Takefumi Kondo
- Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan; The Keihanshin Consortium for Fostering the Next Generation of Global Leaders in Research (K-CONNEX), Sakyo-ku, Kyoto 606-8501, Japan.
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21
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Liu P, Li D, Zhang J, He M, Gao D, Wang Y, Lin Y, Pan D, Li P, Wang T, Li J, Kong F, Zeng B, Lu L, Ma J, Long K, Li G, Tang Q, Jin L, Li M. Comparative three-dimensional genome architectures of adipose tissues provide insight into human-specific regulation of metabolic homeostasis. J Biol Chem 2023; 299:104757. [PMID: 37116707 PMCID: PMC10245122 DOI: 10.1016/j.jbc.2023.104757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 03/22/2023] [Accepted: 04/19/2023] [Indexed: 04/30/2023] Open
Abstract
Elucidating the regulatory mechanisms of human adipose tissues (ATs) evolution is essential for understanding human-specific metabolic regulation, but the functional importance and evolutionary dynamics of three-dimensional (3D) genome organizations of ATs are not well defined. Here, we compared the 3D genome architectures of anatomically distinct ATs from humans and six representative mammalian models. We recognized evolutionarily conserved and human-specific chromatin conformation in ATs at multiple scales, including compartmentalization, topologically associating domain (TAD), and promoter-enhancer interactions (PEI), which have not been described previously. We found PEI are much more evolutionarily dynamic with respect to compartmentalization and topologically associating domain. Compared to conserved PEIs, human-specific PEIs are enriched for human-specific sequence, and the binding motifs of their potential mediators (transcription factors) are less conserved. Our data also demonstrated that genes involved in the evolutionary dynamics of chromatin organization have weaker transcriptional conservation than those associated with conserved chromatin organization. Furthermore, the genes involved in energy metabolism and the maintenance of metabolic homeostasis are enriched in human-specific chromatin organization, while housekeeping genes, health-related genes, and genetic variations are enriched in evolutionarily conserved compared to human-specific chromatin organization. Finally, we showed extensively divergent human-specific 3D genome organizations among one subcutaneous and three visceral ATs. Together, these findings provide a global overview of 3D genome architecture dynamics between ATs from human and mammalian models and new insights into understanding the regulatory evolution of human ATs.
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Affiliation(s)
- Pengliang Liu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Diyan Li
- School of Pharmacy, Chengdu University, Chengdu, Sichuan, China.
| | - Jiaman Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mengnan He
- Wildlife Conservation Research Department, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Dengfeng Gao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yujie Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yu Lin
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Dengke Pan
- Institute of Organ Transplantation, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Penghao Li
- Jinxin Research Institute for Reproductive Medicine & Genetics, Chengdu Xi'nan Gynecology Hospital, Chengdu, Sichuan, China
| | - Tao Wang
- School of Pharmacy, Chengdu University, Chengdu, Sichuan, China
| | - Jing Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Fanli Kong
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bo Zeng
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Lu Lu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jideng Ma
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Keren Long
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Guisen Li
- Renal Department & Nephrology Institute, Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Qianzi Tang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Long Jin
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mingzhou Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China.
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22
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McAllan L, Baranasic D, Villicaña S, Brown S, Zhang W, Lehne B, Adamo M, Jenkinson A, Elkalaawy M, Mohammadi B, Hashemi M, Fernandes N, Lambie N, Williams R, Christiansen C, Yang Y, Zudina L, Lagou V, Tan S, Castillo-Fernandez J, King JWD, Soong R, Elliott P, Scott J, Prokopenko I, Cebola I, Loh M, Lenhard B, Batterham RL, Bell JT, Chambers JC, Kooner JS, Scott WR. Integrative genomic analyses in adipocytes implicate DNA methylation in human obesity and diabetes. Nat Commun 2023; 14:2784. [PMID: 37188674 PMCID: PMC10185556 DOI: 10.1038/s41467-023-38439-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 05/03/2023] [Indexed: 05/17/2023] Open
Abstract
DNA methylation variations are prevalent in human obesity but evidence of a causative role in disease pathogenesis is limited. Here, we combine epigenome-wide association and integrative genomics to investigate the impact of adipocyte DNA methylation variations in human obesity. We discover extensive DNA methylation changes that are robustly associated with obesity (N = 190 samples, 691 loci in subcutaneous and 173 loci in visceral adipocytes, P < 1 × 10-7). We connect obesity-associated methylation variations to transcriptomic changes at >500 target genes, and identify putative methylation-transcription factor interactions. Through Mendelian Randomisation, we infer causal effects of methylation on obesity and obesity-induced metabolic disturbances at 59 independent loci. Targeted methylation sequencing, CRISPR-activation and gene silencing in adipocytes, further identifies regional methylation variations, underlying regulatory elements and novel cellular metabolic effects. Our results indicate DNA methylation is an important determinant of human obesity and its metabolic complications, and reveal mechanisms through which altered methylation may impact adipocyte functions.
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Affiliation(s)
- Liam McAllan
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - Damir Baranasic
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - Sergio Villicaña
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Scarlett Brown
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG, UK
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, Middlesex, UB1 3HW, UK
| | - Benjamin Lehne
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG, UK
| | - Marco Adamo
- UCLH Bariatric Centre for Weight Loss, Weight Management and Metabolic and Endocrine Surgery, University College London Hospitals, Ground Floor West Wing, 250 Euston Road, London, NW1 2PG, UK
| | - Andrew Jenkinson
- UCLH Bariatric Centre for Weight Loss, Weight Management and Metabolic and Endocrine Surgery, University College London Hospitals, Ground Floor West Wing, 250 Euston Road, London, NW1 2PG, UK
| | - Mohamed Elkalaawy
- UCLH Bariatric Centre for Weight Loss, Weight Management and Metabolic and Endocrine Surgery, University College London Hospitals, Ground Floor West Wing, 250 Euston Road, London, NW1 2PG, UK
| | - Borzoueh Mohammadi
- UCLH Bariatric Centre for Weight Loss, Weight Management and Metabolic and Endocrine Surgery, University College London Hospitals, Ground Floor West Wing, 250 Euston Road, London, NW1 2PG, UK
| | - Majid Hashemi
- UCLH Bariatric Centre for Weight Loss, Weight Management and Metabolic and Endocrine Surgery, University College London Hospitals, Ground Floor West Wing, 250 Euston Road, London, NW1 2PG, UK
| | - Nadia Fernandes
- Imperial BRC Genomics Facility, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Nathalie Lambie
- Imperial BRC Genomics Facility, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Richard Williams
- Imperial BRC Genomics Facility, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Colette Christiansen
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, UK
| | - Youwen Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG, UK
- School of Cardiovascular and Metabolic Medicine and Sciences, James Black Centre, King's College London British Heart Foundation Centre of Excellence, 125 Coldharbour Lane, London, SE5 9NU, UK
| | - Liudmila Zudina
- Department of Clinical & Experimental Medicine, University of Surrey, Guildford, UK
| | - Vasiliki Lagou
- Department of Microbiology and Immunology, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
| | - Sili Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | | | - James W D King
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - Richie Soong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Pathology, National University Hospital, Singapore, Singapore
| | - Paul Elliott
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG, UK
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- National Institute for Health Research Biomedical Research Centre, Imperial College London, London, UK
| | - James Scott
- National Heart and Lung Institute, Imperial College London, London, W12 0NN, UK
- Imperial College Healthcare NHS Trust, London, W12 0HS, UK
| | - Inga Prokopenko
- Department of Clinical & Experimental Medicine, University of Surrey, Guildford, UK
- People-Centred Artificial Intelligence Institute, University of Surrey, Guildford, UK
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre Russian Academy of Sciences, Ufa, Russian Federation
| | - Inês Cebola
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Marie Loh
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG, UK
- Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos, Level 5, Singapore, 138648, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Boris Lenhard
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - Rachel L Batterham
- UCLH Bariatric Centre for Weight Loss, Weight Management and Metabolic and Endocrine Surgery, University College London Hospitals, Ground Floor West Wing, 250 Euston Road, London, NW1 2PG, UK
- Centre for Obesity Research, Rayne Institute, Department of Medicine, University College, London, WC1E 6JJ, UK
- National Institute of Health Research University College London Hospitals Biomedical Research Centre, London, W1T 7DN, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - John C Chambers
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG, UK
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, Middlesex, UB1 3HW, UK
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, London, W12 0HS, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, Middlesex, UB1 3HW, UK
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- National Heart and Lung Institute, Imperial College London, London, W12 0NN, UK
- Imperial College Healthcare NHS Trust, London, W12 0HS, UK
| | - William R Scott
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK.
- MRC London Institute of Medical Sciences, London, W12 0NN, UK.
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG, UK.
- Imperial College Healthcare NHS Trust, London, W12 0HS, UK.
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23
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Fu Q, Cheung WA, Majnik AV, Ke X, Pastinen T, Lane RH. Adverse Maternal Environments Perturb Hepatic DNA Methylome and Transcriptome Prior to the Adult-Onset Non-Alcoholic Fatty Liver Disease in Mouse Offspring. Nutrients 2023; 15:2167. [PMID: 37432267 DOI: 10.3390/nu15092167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/24/2023] [Accepted: 04/28/2023] [Indexed: 07/12/2023] Open
Abstract
Exposure to adverse early-life environments (AME) increases the incidence of developing adult-onset non-alcoholic fatty liver disease (NAFLD). DNA methylation has been postulated to link AME and late-onset diseases. This study aimed to investigate whether and to what extent the hepatic DNA methylome was perturbed prior to the development of NAFLD in offspring exposed to AME in mice. AME constituted maternal Western diet and late-gestational stress. Male offspring livers at birth (d0) and weaning (d21) were used for evaluating the DNA methylome and transcriptome using the reduced representation of bisulfite sequencing and RNA-seq, respectively. We found AME caused 5879 differentially methylated regions (DMRs) and zero differentially expressed genes (DEGs) at d0 and 2970 and 123, respectively, at d21. The majority of the DMRs were distal to gene transcription start sites and did not correlate with DEGs. The DEGs at d21 were significantly enriched in GO biological processes characteristic of liver metabolic functions. In conclusion, AME drove changes in the hepatic DNA methylome, which preceded perturbations in the hepatic metabolic transcriptome, which preceded the onset of NAFLD. We speculate that subtle impacts on dynamic enhancers lead to long-range regulatory changes that manifest over time as gene network alternations and increase the incidence of NAFLD later in life.
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Affiliation(s)
- Qi Fu
- Department of Research Administration, Children's Mercy Hospital, Kansas City, MO 64108, USA
| | - Warren A Cheung
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, MO 64108, USA
| | - Amber V Majnik
- Department of Pediatrics, Medical College of Wisconsin, 8701 W Watertown Plank Rd., Milwaukee, WI 53226, USA
| | - Xingrao Ke
- Department of Research Administration, Children's Mercy Hospital, Kansas City, MO 64108, USA
| | - Tomi Pastinen
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, MO 64108, USA
| | - Robert H Lane
- Department of Administration, Children's Mercy Hospital, Kansas City, MO 64108, USA
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24
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Sahana TG, Chase KJ, Liu F, Lloyd TE, Rossoll W, Zhang K. c-Jun N-Terminal Kinase Promotes Stress Granule Assembly and Neurodegeneration in C9orf72-Mediated ALS and FTD. J Neurosci 2023; 43:3186-3197. [PMID: 37015810 PMCID: PMC10146492 DOI: 10.1523/jneurosci.1799-22.2023] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 02/09/2023] [Accepted: 03/15/2023] [Indexed: 04/06/2023] Open
Abstract
Stress granules are the RNA/protein condensates assembled in the cells under stress. They play a critical role in the pathogenesis of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). However, how stress granule assembly is regulated and related to ALS/FTD pathomechanism is incompletely understood. Mutation in the C9orf72 gene is the most common cause of familial ALS and FTD. C9orf72 mutation causes the formation of toxic dipeptide repeats. Here we show that the two most toxic dipeptide repeats [i.e., poly(GR) and poly(PR)] activate c-Jun N-terminal kinase (JNK) via the ER-stress response protein IRE1 using fly and cellular models. Further, we show that activated JNK promotes stress granule assembly in cells by promoting the transcription of one of the key stress granule proteins (i.e., G3BP1) by inducing histone 3 phosphorylation. Consistent with these findings, JNK or IRE1 inhibition reduced stress granule formation, histone 3 phosphorylation, G3BP1 mRNA and protein levels, and neurotoxicity in cells overexpressing poly(GR) and poly(PR) or neurons derived from male and female C9ALS/FTD patient-induced pluripotent stem cells. Our findings connect ER stress, JNK activation, and stress granule assembly in a unified pathway contributing to C9ALS/FTD neurodegeneration.SIGNIFICANCE STATEMENT c-Jun N-terminal kinase (JNK) is a part of the mitogen-activated protein kinase pathway, which is the central node for the integration of multiple stress signals. Cells are under constant stress in neurodegenerative diseases, and how these cells respond to stress signals is a critical factor in determining their survival or death. Previous studies have shown JNK as a major contributor to cellular apoptosis. Here, we show the role of JNK in stress granule assembly. We identify that toxic dipeptide repeats produced in ALS/FTD conditions activate JNK. The activated JNK in the nucleus can induce histone modifications which increase G3BP1 expression, thus promoting stress granule assembly and neurodegeneration.
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Affiliation(s)
| | | | - Feilin Liu
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida 32224
| | - Thomas E Lloyd
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205
| | - Wilfried Rossoll
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida 32224
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, Florida 32224
| | - Ke Zhang
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida 32224
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, Florida 32224
- Institute of Neurological and Psychiatric Disorders, Shenzhen Bay Laboratory, Gaoke Innovation Centre A16, Guangqiao Rd, Shenzhen, Guangdong 518107, China, P.R
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25
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Yang J, Chen Y, Jing Y, Green MR, Han L. Advancing CAR T cell therapy through the use of multidimensional omics data. Nat Rev Clin Oncol 2023; 20:211-228. [PMID: 36721024 DOI: 10.1038/s41571-023-00729-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2023] [Indexed: 02/01/2023]
Abstract
Despite the notable success of chimeric antigen receptor (CAR) T cell therapies in the treatment of certain haematological malignancies, challenges remain in optimizing CAR designs and cell products, improving response rates, extending the durability of remissions, reducing toxicity and broadening the utility of this therapeutic modality to other cancer types. Data from multidimensional omics analyses, including genomics, epigenomics, transcriptomics, T cell receptor-repertoire profiling, proteomics, metabolomics and/or microbiomics, provide unique opportunities to dissect the complex and dynamic multifactorial phenotypes, processes and responses of CAR T cells as well as to discover novel tumour targets and pathways of resistance. In this Review, we summarize the multidimensional cellular and molecular profiling technologies that have been used to advance our mechanistic understanding of CAR T cell therapies. In addition, we discuss current applications and potential strategies leveraging multi-omics data to identify optimal target antigens and other molecular features that could be exploited to enhance the antitumour activity and minimize the toxicity of CAR T cell therapy. Indeed, fully utilizing multi-omics data will provide new insights into the biology of CAR T cell therapy, further accelerate the development of products with improved efficacy and safety profiles, and enable clinicians to better predict and monitor patient responses.
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Affiliation(s)
- Jingwen Yang
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Yamei Chen
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Ying Jing
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Michael R Green
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Leng Han
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA.
- Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX, USA.
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26
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Hey J, Halperin C, Hartmann M, Mayer S, Schönung M, Lipka DB, Scherz-Shouval R, Plass C. DNA methylation landscape of tumor-associated macrophages reveals pathways, transcription factors and prognostic value relevant to triple-negative breast cancer patients. Int J Cancer 2023; 152:1226-1242. [PMID: 36408934 DOI: 10.1002/ijc.34364] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 10/17/2022] [Accepted: 11/03/2022] [Indexed: 11/23/2022]
Abstract
The accumulation of myeloid cells, particularly tumor-associated macrophages (TAMs), characterizes the tumor microenvironment (TME) of many solid cancers, including breast cancer. Compared to healthy tissue-resident macrophages, TAMs acquire distinct transcriptomes and tumor-promoting functions by largely unknown mechanisms. Here, we hypothesize the involvement of TME signaling and subsequent epigenetic reprogramming of TAMs. Using the 4T1 mouse model of triple-negative breast cancer, we demonstrate that the presence of cancer cells significantly alters the DNA methylation landscape of macrophages and, to a lesser extent, bone marrow-derived monocytes (BMDMs). TAM methylomes, dissected into BMDM-originating and TAM-specific epigenetic programs, implicated transcription factors (TFs) and signaling pathways involved in TAM reprogramming, correlated with cancer-specific gene expression patterns. Utilizing published single-cell gene expression data, we linked microenvironmentally-derived signals to the cancer-specific DNA methylation landscape of TAMs. These integrative analyses highlighted the role of altered cytokine production in the TME (eg, TGF-β, IFN-γ and CSF1) on the induction of specific TFs (eg, FOSL2, STAT1 and RUNX3) responsible for the epigenetic reprogramming of TAMs. DNA methylation deconvolution identified a TAM-specific signature associated with the identified signaling pathways and TFs, corresponding with severe tumor grade and poor prognosis of breast cancer patients. Similarly, immunosuppressive TAM functions were identified, such as induction of the immune inhibitory receptor-ligand PD-L1 by DNA hypomethylation of Cd274. Collectively, these results provide strong evidence that the epigenetic landscapes of macrophages and monocytes are perturbed by the presence of breast cancer, pointing to molecular mechanisms of TAM reprogramming, impacting patient outcomes.
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Affiliation(s)
- Joschka Hey
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Faculty of Biosciences, Ruprecht Karl University of Heidelberg, Heidelberg, Germany
| | - Coral Halperin
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Mark Hartmann
- Translational Cancer Epigenomics, Division Translational Medical Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Shimrit Mayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Maximilian Schönung
- Faculty of Biosciences, Ruprecht Karl University of Heidelberg, Heidelberg, Germany.,Translational Cancer Epigenomics, Division Translational Medical Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Daniel B Lipka
- Translational Cancer Epigenomics, Division Translational Medical Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Ruth Scherz-Shouval
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
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27
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Islam S, Mukherjee C. Molecular regulation of hypoxia through the lenses of noncoding RNAs and epitranscriptome. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1750. [PMID: 35785444 DOI: 10.1002/wrna.1750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 05/27/2022] [Accepted: 06/06/2022] [Indexed: 11/09/2022]
Abstract
Cells maintain homeostasis in response to environmental stress through specific cell stress responses. Hypoxic stress, well known to be associated with diverse solid tumors, is one of the main reasons for cancer-related mortality. Although cells can balance themselves well during hypoxic stress, the underlying molecular mechanisms are not well understood. The enhanced appreciation of diverse roles played by noncoding transcriptome and epigenome in recent years has brought to light the involvement of noncoding RNAs and epigenetic modifiers in hypoxic regulation. The emergence of techniques like deep sequencing has facilitated the identification of large numbers of long noncoding RNAs (lncRNAs) that are differentially regulated in various cancers. Similarly, proteomic studies have identified diverse epigenetic modifiers such as HATs, HDACs, DNMTs, polycomb groups of proteins, and their possible roles in the regulation of hypoxia. The crosstalk between lncRNAs and epigenetic modifiers play a pivotal role in hypoxia-induced cancer initiation and progression. Besides the lncRNAs, several other noncoding RNAs like circular RNAs, miRNAs, and so forth are also expressed during hypoxic conditions. Hypoxia has a profound effect on the expression of noncoding RNAs and epigenetic modifiers. Conversely, noncoding RNAs/epigenetic modifies can regulate the hypoxia signaling axis by modulating the stability of the hypoxia-inducible factors (HIFs). The focus of this review is to illustrate the molecular orchestration underlying hypoxia biology, especially in cancers, which can help in identifying promising therapeutic targets in hypoxia-induced cancers. This article is categorized under: RNA Turnover and Surveillance > Regulation of RNA Stability RNA in Disease and Development > RNA in Disease RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry.
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Affiliation(s)
- Safirul Islam
- Institute of Health Sciences (erstwhile School of Biotechnology), Presidency University, Kolkata, India
| | - Chandrama Mukherjee
- Institute of Health Sciences (erstwhile School of Biotechnology), Presidency University, Kolkata, India
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28
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Advances in the Histone Acetylation Modification in the Oral Squamous Cell Carcinoma. JOURNAL OF ONCOLOGY 2023. [DOI: 10.1155/2023/4616682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Oral squamous cell carcinoma (OSCC) is one of the common malignant tumors in the head and neck, characterized by high malignancy, rapid growth and metastasis, high invasive ability, and high mortality. In recent years, surgery combined with chemotherapy or radiotherapy remains the preferred clinical treatment for OSCC, despite considerable advances in diagnostic and therapeutic techniques. Hence, new targeted therapy is urgently needed. Histone modification affects the function of massive cells through histone acetyltransferase and histone deacetylase. Accompanied by the progress of some diseases, especially tumors, these proteins often show abnormal functions, and by reversing these abnormalities with drugs or gene therapy, the cancer phenotype can even be restored to normal. As a result, they are potential drug targets. This article reviewed the role of the histone dynamic process of acetylation modifications and their associated active modifying enzymes in the pathogenesis and progress of OSCC. Moreover, we explored the value of histone acetylation modification as a potential therapeutic target and the new progress of related drugs in clinical treatment.
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29
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Abstract
The epitranscriptome, defined as RNA modifications that do not involve alterations in the nucleotide sequence, is a popular topic in the genomic sciences. Because we need massive computational techniques to identify epitranscriptomes within individual transcripts, many tools have been developed to infer epitranscriptomic sites as well as to process datasets using high-throughput sequencing. In this review, we summarize recent developments in epitranscriptome spatial detection and data analysis and discuss their progression.
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Affiliation(s)
- Y-H Taguchi
- Department of Physics, Chuo University, Tokyo, Japan
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30
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Ge T, Gu X, Jia R, Ge S, Chai P, Zhuang A, Fan X. Crosstalk between metabolic reprogramming and epigenetics in cancer: updates on mechanisms and therapeutic opportunities. CANCER COMMUNICATIONS (LONDON, ENGLAND) 2022; 42:1049-1082. [PMID: 36266736 PMCID: PMC9648395 DOI: 10.1002/cac2.12374] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 09/19/2022] [Accepted: 10/10/2022] [Indexed: 11/24/2022]
Abstract
Reversible, spatial, and temporal regulation of metabolic reprogramming and epigenetic homeostasis are prominent hallmarks of carcinogenesis. Cancer cells reprogram their metabolism to meet the high bioenergetic and biosynthetic demands for vigorous proliferation. Epigenetic dysregulation is a common feature of human cancers, which contributes to tumorigenesis and maintenance of the malignant phenotypes by regulating gene expression. The epigenome is sensitive to metabolic changes. Metabolism produces various metabolites that are substrates, cofactors, or inhibitors of epigenetic enzymes. Alterations in metabolic pathways and fluctuations in intermediate metabolites convey information regarding the intracellular metabolic status into the nucleus by modulating the activity of epigenetic enzymes and thus remodeling the epigenetic landscape, inducing transcriptional responses to heterogeneous metabolic requirements. Cancer metabolism is regulated by epigenetic machinery at both transcriptional and post‐transcriptional levels. Epigenetic modifiers, chromatin remodelers and non‐coding RNAs are integral contributors to the regulatory networks involved in cancer metabolism, facilitating malignant transformation. However, the significance of the close connection between metabolism and epigenetics in the context of cancer has not been fully deciphered. Thus, it will be constructive to summarize and update the emerging new evidence supporting this bidirectional crosstalk and deeply assess how the crosstalk between metabolic reprogramming and epigenetic abnormalities could be exploited to optimize treatment paradigms and establish new therapeutic options. In this review, we summarize the central mechanisms by which epigenetics and metabolism reciprocally modulate each other in cancer and elaborate upon and update the major contributions of the interplays between epigenetic aberrations and metabolic rewiring to cancer initiation and development. Finally, we highlight the potential therapeutic opportunities for hematological malignancies and solid tumors by targeting this epigenetic‐metabolic circuit. In summary, we endeavored to depict the current understanding of the coordination between these fundamental abnormalities more comprehensively and provide new perspectives for utilizing metabolic and epigenetic targets for cancer treatment.
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Affiliation(s)
- Tongxin Ge
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, P. R. China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, P. R. China
| | - Xiang Gu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, P. R. China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, P. R. China
| | - Renbing Jia
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, P. R. China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, P. R. China
| | - Shengfang Ge
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, P. R. China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, P. R. China
| | - Peiwei Chai
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, P. R. China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, P. R. China
| | - Ai Zhuang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, P. R. China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, P. R. China
| | - Xianqun Fan
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, P. R. China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, P. R. China
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31
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Zare Harofte S, Soltani M, Siavashy S, Raahemifar K. Recent Advances of Utilizing Artificial Intelligence in Lab on a Chip for Diagnosis and Treatment. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2203169. [PMID: 36026569 DOI: 10.1002/smll.202203169] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 07/16/2022] [Indexed: 05/14/2023]
Abstract
Nowadays, artificial intelligence (AI) creates numerous promising opportunities in the life sciences. AI methods can be significantly advantageous for analyzing the massive datasets provided by biotechnology systems for biological and biomedical applications. Microfluidics, with the developments in controlled reaction chambers, high-throughput arrays, and positioning systems, generate big data that is not necessarily analyzed successfully. Integrating AI and microfluidics can pave the way for both experimental and analytical throughputs in biotechnology research. Microfluidics enhances the experimental methods and reduces the cost and scale, while AI methods significantly improve the analysis of huge datasets obtained from high-throughput and multiplexed microfluidics. This review briefly presents a survey of the role of AI and microfluidics in biotechnology. Also, the incorporation of AI with microfluidics is comprehensively investigated. Specifically, recent studies that perform flow cytometry cell classification, cell isolation, and a combination of them by gaining from both AI methods and microfluidic techniques are covered. Despite all current challenges, various fields of biotechnology can be remarkably affected by the combination of AI and microfluidic technologies. Some of these fields include point-of-care systems, precision, personalized medicine, regenerative medicine, prognostics, diagnostics, and treatment of oncology and non-oncology-related diseases.
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Affiliation(s)
- Samaneh Zare Harofte
- Department of Mechanical Engineering, K. N. Toosi University of Technology, Tehran, 19967-15433, Iran
| | - Madjid Soltani
- Department of Mechanical Engineering, K. N. Toosi University of Technology, Tehran, 19967-15433, Iran
- Department of Electrical and Computer Engineering, Faculty of Engineering, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
- Centre for Biotechnology and Bioengineering (CBB), University of Waterloo, Waterloo, ON, N2L 3G1, Canada
- Advanced Bioengineering Initiative Center, Multidisciplinary International Complex, K. N. Toosi University of Technology, Tehran, 14176-14411, Iran
- Cancer Biology Research Center, Cancer Institute of Iran, Tehran University of Medical Sciences, Tehran, 14197-33141, Iran
| | - Saeed Siavashy
- Department of Mechanical Engineering, K. N. Toosi University of Technology, Tehran, 19967-15433, Iran
| | - Kaamran Raahemifar
- Data Science and Artificial Intelligence Program, College of Information Sciences and Technology (IST), Penn State University, State College, PA, 16801, USA
- School of Optometry and Vision Science, Faculty of Science, University of Waterloo, 200 University Ave. W, Waterloo, ON, N2L 3G1, Canada
- Department of Chemical Engineering, Faculty of Engineering, University of Waterloo, 200 University Ave. W, Waterloo, ON, N2L 3G1, Canada
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32
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Li R, Meng S, Ji M, Rong X, You Z, Cai C, Guo X, Lu C, Liang G, Cao G, Li B, Yang Y. HMG20A Inhibit Adipogenesis by Transcriptional and Epigenetic Regulation of MEF2C Expression. Int J Mol Sci 2022; 23:ijms231810559. [PMID: 36142473 PMCID: PMC9505946 DOI: 10.3390/ijms231810559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/29/2022] [Accepted: 09/04/2022] [Indexed: 11/24/2022] Open
Abstract
Obesity and its associated metabolic disease do serious harm to human health. The transcriptional cascade network with transcription factors as the core is the focus of current research on adipogenesis and its mechanism. Previous studies have found that HMG domain protein 20A (HMG20A) is highly expressed in the early stage of adipogenic differentiation of porcine intramuscular fat (IMF), which may be involved in regulating adipogenesis. In this study, HMG20A was found to play a key negative regulatory role in adipogenesis. Gain- and loss-of-function studies revealed that HMG20A inhibited the differentiation of SVF cells and C3H10T1/2 cells into mature adipocytes. RNA-seq was used to screen differentially expressed genes after HMG20A knockdown. qRT-PCR and ChIP-PCR confirmed that MEF2C was the real target of HMG20A, and HMG20A played a negative regulatory role through MEF2C. HMG20A binding protein LSD1 was found to alleviate the inhibitory effect of HMG20A on adipogenesis. Further studies showed that HMG20A could cooperate with LSD1 to increase the H3K4me2 of the MEF2C promoter and then increase the expression of MEF2C. Collectively, these findings highlight a role for HMG20A-dependent transcriptional and epigenetic regulation in adipogenesis.
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33
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Lei L, Jiang L, Hu Y, Chen M, Huang J, Chen J, Zeng Q. The comprehensive assessment of epigenetics changes during skin development. FUNDAMENTAL RESEARCH 2022. [DOI: 10.1016/j.fmre.2022.08.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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McKinney BC, McClain LL, Hensler CM, Wei Y, Klei L, Lewis DA, Devlin B, Wang J, Ding Y, Sweet RA. Schizophrenia-associated differential DNA methylation in brain is distributed across the genome and annotated to MAD1L1, a locus at which DNA methylation and transcription phenotypes share genetic variation with schizophrenia risk. Transl Psychiatry 2022; 12:340. [PMID: 35987687 PMCID: PMC9392724 DOI: 10.1038/s41398-022-02071-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/21/2022] [Accepted: 07/15/2022] [Indexed: 11/09/2022] Open
Abstract
DNA methylation (DNAm), the addition of a methyl group to a cytosine in DNA, plays an important role in the regulation of gene expression. Single-nucleotide polymorphisms (SNPs) associated with schizophrenia (SZ) by genome-wide association studies (GWAS) often influence local DNAm levels. Thus, DNAm alterations, acting through effects on gene expression, represent one potential mechanism by which SZ-associated SNPs confer risk. In this study, we investigated genome-wide DNAm in postmortem superior temporal gyrus from 44 subjects with SZ and 44 non-psychiatric comparison subjects using Illumina Infinium MethylationEPIC BeadChip microarrays, and extracted cell-type-specific methylation signals by applying tensor composition analysis. We identified SZ-associated differential methylation at 242 sites, and 44 regions containing two or more sites (FDR cutoff of q = 0.1) and determined a subset of these were cell-type specific. We found mitotic arrest deficient 1-like 1 (MAD1L1), a gene within an established GWAS risk locus, harbored robust SZ-associated differential methylation. We investigated the potential role of MAD1L1 DNAm in conferring SZ risk by assessing for colocalization among quantitative trait loci for methylation and gene transcripts (mQTLs and tQTLs) in brain tissue and GWAS signal at the locus using multiple-trait-colocalization analysis. We found that mQTLs and tQTLs colocalized with the GWAS signal (posterior probability >0.8). Our findings suggest that alterations in MAD1L1 methylation and transcription may mediate risk for SZ at the MAD1L1-containing locus. Future studies to identify how SZ-associated differential methylation affects MAD1L1 biological function are indicated.
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Affiliation(s)
- Brandon C McKinney
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA.
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Lora L McClain
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Christopher M Hensler
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yue Wei
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lambertus Klei
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - David A Lewis
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jiebiao Wang
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ying Ding
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Robert A Sweet
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA.
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA.
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA.
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35
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Maldonato BJ, Vergara AG, Yadav J, Glass SM, Paragas EM, Li D, Lazarus P, McClay JL, Ning B, Daly AK, Russell LE. Epigenetics in drug disposition & drug therapy: symposium report of the 24 th North American meeting of the International Society for the Study of Xenobiotics (ISSX). Drug Metab Rev 2022; 54:318-330. [PMID: 35876105 PMCID: PMC9970013 DOI: 10.1080/03602532.2022.2101662] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 07/10/2022] [Indexed: 11/03/2022]
Abstract
The 24th North American International Society for the Study of Xenobiotics (ISSX) meeting, held virtually from September 13 to 17, 2021, embraced the theme of "Broadening Our Horizons." This reinforces a key mission of ISSX: striving to share innovative science related to drug discovery and development. Session speakers and the ISSX New Investigators Group, which supports the scientific and professional development of student and early career ISSX members, elected to highlight the scientific content presented during the captivating session titled, "Epigenetics in Drug Disposition & Drug Therapy." The impact genetic variation has on drug response is well established; however, this session underscored the importance of investigating the role of epigenetics in drug disposition and drug discovery. Session speakers, Drs. Ning, McClay, and Lazarus, detailed mechanisms by which epigenetic players including long non-coding RNA (lncRNAs), microRNA (miRNAs), DNA methylation, and histone acetylation can alter the expression of genes involved in pharmacokinetics, pharmacodynamics, and toxicity. Dr. Ning detailed current knowledge about miRNAs and lncRNAs and the mechanisms by which they can affect the expression of drug metabolizing enzymes (DMEs) and nuclear receptors. Dr. Lazarus discussed the potential role of miRNAs on UDP-glucuronosyltransferase (UGT) expression and activity. Dr. McClay provided evidence that aging alters methylation and acetylation of DMEs in the liver, affecting gene expression and activity. These topics, compiled by the symposium organizers, presenters, and the ISSX New Investigators Group, are herein discussed, along with exciting future perspectives for epigenetics in drug disposition and drug discovery research.
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Affiliation(s)
- Benjamin J Maldonato
- Department of Nonclinical Development and Clinical Pharmacology, Revolution Medicines, Inc, Redwood City, CA, United States
| | - Ana G Vergara
- Department of ADME & Discovery Toxicology, Merck & Co., Inc, Rahway, NJ, United States
| | - Jaydeep Yadav
- Department of ADME & Discovery Toxicology, Merck & Co., Inc, Rahway, NJ, United States
| | - Sarah M Glass
- Janssen Research & Development, San Diego, CA, United States
| | | | - Dongying Li
- National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA), Jefferson, AR, United States
| | - Philip Lazarus
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, WA, United States
| | - Joseph L McClay
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, United States
| | - Baitang Ning
- National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA), Jefferson, AR, United States
| | - Ann K Daly
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Laura E Russell
- Drug Metabolism and Pharmacokinetics, AbbVie Inc, North Chicago, Illinois, United States
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36
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Wu S, Yin Y, Wang X. The epigenetic regulation of the germinal center response. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194828. [PMID: 35643396 DOI: 10.1016/j.bbagrm.2022.194828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 05/22/2022] [Indexed: 06/15/2023]
Abstract
In response to T-cell-dependent antigens, antigen-experienced B cells migrate to the center of the B-cell follicle to seed the germinal center (GC) response after cognate interactions with CD4+ T cells. These GC B cells eventually mature into memory and long-lived antibody-secreting plasma cells, thus generating long-lived humoral immunity. Within GC, B cells undergo somatic hypermutation of their B cell receptors (BCR) and positive selection for the emergence of high-affinity antigen-specific B-cell clones. However, this process may be dangerous, as the accumulation of aberrant mutations could result in malignant transformation of GC B cells or give rise to autoreactive B cell clones that can cause autoimmunity. Because of this, better understanding of GC development provides diagnostic and therapeutic clues to the underlying pathologic process. A productive GC response is orchestrated by multiple mechanisms. An emerging important regulator of GC reaction is epigenetic modulation, which has key transcriptional regulatory properties. In this review, we summarize the current knowledge on the biology of epigenetic mechanisms in the regulation of GC reaction and outline its importance in identification of immunotherapy decision making.
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Affiliation(s)
- Shusheng Wu
- Department of Immunology, State Key Laboratory of Reproductive Medicine, NHC Key Laboratory of Antibody Technique, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yuye Yin
- Department of Immunology, State Key Laboratory of Reproductive Medicine, NHC Key Laboratory of Antibody Technique, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiaoming Wang
- Department of Immunology, State Key Laboratory of Reproductive Medicine, NHC Key Laboratory of Antibody Technique, Nanjing Medical University, Nanjing, Jiangsu, China.
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37
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Ljungman M. Transcription and genome integrity. DNA Repair (Amst) 2022; 118:103373. [PMID: 35914488 DOI: 10.1016/j.dnarep.2022.103373] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 07/16/2022] [Accepted: 07/17/2022] [Indexed: 11/03/2022]
Abstract
Transcription can cause genome instability by promoting R-loop formation but also act as a mutation-suppressing machinery by sensing of DNA lesions leading to the activation of DNA damage signaling and transcription-coupled repair. Recovery of RNA synthesis following the resolution of repair of transcription-blocking lesions is critical to avoid apoptosis and several new factors involved in this process have recently been identified. Some DNA repair proteins are recruited to initiating RNA polymerases and this may expediate the recruitment of other factors that participate in the repair of transcription-blocking DNA lesions. Recent studies have shown that transcription of protein-coding genes does not always give rise to spliced transcripts, opening the possibility that cells may use the transcription machinery in a splicing-uncoupled manner for other purposes including surveillance of the transcribed genome.
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Affiliation(s)
- Mats Ljungman
- Departments of Radiation Oncology and Environmental Health Sciences, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA.
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38
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Zhou W, Hinoue T, Barnes B, Mitchell O, Iqbal W, Lee SM, Foy KK, Lee KH, Moyer EJ, VanderArk A, Koeman JM, Ding W, Kalkat M, Spix NJ, Eagleson B, Pospisilik JA, Szabó PE, Bartolomei MS, Vander Schaaf NA, Kang L, Wiseman AK, Jones PA, Krawczyk CM, Adams M, Porecha R, Chen BH, Shen H, Laird PW. DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse. CELL GENOMICS 2022; 2:100144. [PMID: 35873672 PMCID: PMC9306256 DOI: 10.1016/j.xgen.2022.100144] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/20/2022] [Accepted: 05/20/2022] [Indexed: 05/21/2023]
Abstract
We have developed a mouse DNA methylation array that contains 296,070 probes representing the diversity of mouse DNA methylation biology. We present a mouse methylation atlas as a rich reference resource of 1,239 DNA samples encompassing distinct tissues, strains, ages, sexes, and pathologies. We describe applications for comparative epigenomics, genomic imprinting, epigenetic inhibitors, patient-derived xenograft assessment, backcross tracing, and epigenetic clocks. We dissect DNA methylation processes associated with differentiation, aging, and tumorigenesis. Notably, we find that tissue-specific methylation signatures localize to binding sites for transcription factors controlling the corresponding tissue development. Age-associated hypermethylation is enriched at regions of Polycomb repression, while hypomethylation is enhanced at regions bound by cohesin complex members. Apc Min/+ polyp-associated hypermethylation affects enhancers regulating intestinal differentiation, while hypomethylation targets AP-1 binding sites. This Infinium Mouse Methylation BeadChip (version MM285) is widely accessible to the research community and will accelerate high-sample-throughput studies in this important model organism.
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Affiliation(s)
- Wanding Zhou
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Corresponding author
| | - Toshinori Hinoue
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Bret Barnes
- Illumina, Inc., Bioinformatics and Instrument Software Department, San Diego, CA 92122, USA
| | - Owen Mitchell
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Waleed Iqbal
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sol Moe Lee
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kelly K. Foy
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Kwang-Ho Lee
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Ethan J. Moyer
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alexandra VanderArk
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Julie M. Koeman
- Genomics Core, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Wubin Ding
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Manpreet Kalkat
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Nathan J. Spix
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Bryn Eagleson
- Vivarium and Transgenics Core, Van Andel Institute, Grand Rapids, MI 49503, USA
| | | | - Piroska E. Szabó
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Marisa S. Bartolomei
- Department of Cell and Developmental Biology, Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | | | - Liang Kang
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Ashley K. Wiseman
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Peter A. Jones
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Connie M. Krawczyk
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Marie Adams
- Genomics Core, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Rishi Porecha
- Illumina, Inc., Bioinformatics and Instrument Software Department, San Diego, CA 92122, USA
| | | | - Hui Shen
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
- Corresponding author
| | - Peter W. Laird
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
- Corresponding author
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39
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Lorzadeh A, Hammond C, Wang F, Knapp DJHF, Wong JC, Zhu JYA, Cao Q, Heravi-Moussavi A, Carles A, Wong M, Sharafian Z, Steif J, Moksa M, Bilenky M, Lavoie PM, Eaves CJ, Hirst M. Polycomb contraction differentially regulates terminal human hematopoietic differentiation programs. BMC Biol 2022; 20:104. [PMID: 35550087 PMCID: PMC9102747 DOI: 10.1186/s12915-022-01315-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/28/2022] [Indexed: 12/05/2022] Open
Abstract
Background Lifelong production of the many types of mature blood cells from less differentiated progenitors is a hierarchically ordered process that spans multiple cell divisions. The nature and timing of the molecular events required to integrate the environmental signals, transcription factor activity, epigenetic modifications, and changes in gene expression involved are thus complex and still poorly understood. To address this gap, we generated comprehensive reference epigenomes of 8 phenotypically defined subsets of normal human cord blood. Results We describe a striking contraction of H3K27me3 density in differentiated myelo-erythroid cells that resembles a punctate pattern previously ascribed to pluripotent embryonic stem cells. Phenotypically distinct progenitor cell types display a nearly identical repressive H3K27me3 signature characterized by large organized chromatin K27-modification domains that are retained by mature lymphoid cells but lost in terminally differentiated monocytes and erythroblasts. We demonstrate that inhibition of polycomb group members predicted to control large organized chromatin K27-modification domains influences lymphoid and myeloid fate decisions of primary neonatal hematopoietic progenitors in vitro. We further show that a majority of active enhancers appear in early progenitors, a subset of which are DNA hypermethylated and become hypomethylated and induced during terminal differentiation. Conclusion Primitive human hematopoietic cells display a unique repressive H3K27me3 signature that is retained by mature lymphoid cells but is lost in monocytes and erythroblasts. Intervention data implicate that control of this chromatin state change is a requisite part of the process whereby normal human hematopoietic progenitor cells make lymphoid and myeloid fate decisions. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01315-1.
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Affiliation(s)
- A Lorzadeh
- Department of Microbiology and Immunology, Michael Smith Laboratories, UBC, Vancouver, Canada
| | - C Hammond
- Terry Fox Laboratory, BC Cancer, Vancouver, Canada.,Department of Medicine, UBC, Vancouver, Canada
| | - F Wang
- Terry Fox Laboratory, BC Cancer, Vancouver, Canada.,Department of Medical Genetics, UBC, Vancouver, Canada
| | - D J H F Knapp
- Terry Fox Laboratory, BC Cancer, Vancouver, Canada.,Department of Medicine, UBC, Vancouver, Canada
| | - J Ch Wong
- Department of Microbiology and Immunology, Michael Smith Laboratories, UBC, Vancouver, Canada
| | - J Y A Zhu
- Department of Microbiology and Immunology, Michael Smith Laboratories, UBC, Vancouver, Canada
| | - Q Cao
- Department of Microbiology and Immunology, Michael Smith Laboratories, UBC, Vancouver, Canada
| | - A Heravi-Moussavi
- Canada's Michael Smith Genome Science Centre, BC Cancer, Vancouver, Canada
| | - A Carles
- Department of Microbiology and Immunology, Michael Smith Laboratories, UBC, Vancouver, Canada
| | - M Wong
- Department of Microbiology and Immunology, Michael Smith Laboratories, UBC, Vancouver, Canada
| | - Z Sharafian
- BC Children's Hospital Research Institute, Department of Pediatrics, UBC, Vancouver, Canada
| | - J Steif
- Department of Microbiology and Immunology, Michael Smith Laboratories, UBC, Vancouver, Canada
| | - M Moksa
- Department of Microbiology and Immunology, Michael Smith Laboratories, UBC, Vancouver, Canada
| | - M Bilenky
- Canada's Michael Smith Genome Science Centre, BC Cancer, Vancouver, Canada
| | - P M Lavoie
- BC Children's Hospital Research Institute, Department of Pediatrics, UBC, Vancouver, Canada
| | - C J Eaves
- Terry Fox Laboratory, BC Cancer, Vancouver, Canada.,Department of Medicine, UBC, Vancouver, Canada.,Department of Medical Genetics, UBC, Vancouver, Canada
| | - M Hirst
- Department of Microbiology and Immunology, Michael Smith Laboratories, UBC, Vancouver, Canada. .,Canada's Michael Smith Genome Science Centre, BC Cancer, Vancouver, Canada.
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40
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Lapehn S, Paquette AG. The Placental Epigenome as a Molecular Link Between Prenatal Exposures and Fetal Health Outcomes Through the DOHaD Hypothesis. Curr Environ Health Rep 2022; 9:490-501. [PMID: 35488174 PMCID: PMC9363315 DOI: 10.1007/s40572-022-00354-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2022] [Indexed: 12/31/2022]
Abstract
Purpose of Review The developmental origins of health and disease (DOHaD) hypothesis posits that the perinatal environment can impact fetal and later life health. The placenta is uniquely situated to assess prenatal exposures in the context of DOHaD because it is an essential ephemeral fetal organ that manages the transport of oxygen, nutrients, waste, and endocrine signals between the mother and fetus. The purpose of this review is to summarize recent studies that evaluated the DOHaD hypothesis in human placentas using epigenomics, including DNA methylation and transcriptomic studies of mRNA, lncRNA, and microRNAs. Recent Findings Between 2016 and 2021, 28 articles evaluated associations between prenatal exposures and placental epigenomics across broad exposure categories including maternal smoking, psychosocial stressors, chemicals, air pollution, and metals. Sixteen of these studies connected exposures to health outcome such as birth weight, fetal growth, or infant neurobehavior through mediation analysis, identification of shared associations between exposure and outcome, or network analysis. These aspects of infant and childhood health serve as a foundation for future studies that aim to use placental epigenetics to understand relationships between the prenatal environment and perinatal complications (such as preterm birth or fetal growth restriction) or later life childhood health. Summary Placental DNA methylation and RNA expression have been linked to numerous prenatal exposures, such as PM2.5 air pollution, metals, and maternal smoking, as well as infant and childhood health outcomes, including fetal growth and birth weight. Placental epigenomics provides a unique opportunity to expand the DOHaD premise, particularly if research applies novel methodologies such as multi-omics analysis, sequencing of non-coding RNAs, mixtures analysis, and assessment of health outcomes beyond early childhood.
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Affiliation(s)
- Samantha Lapehn
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, 1900 9th Avenue, Seattle, WA, 98101, USA
| | - Alison G Paquette
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, 1900 9th Avenue, Seattle, WA, 98101, USA. .,Department of Pediatrics, University of Washington, Seattle, WA, USA.
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41
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Yang H, Sun Y, Li Q, Jin F, Dai Y. Diverse Epigenetic Regulations of Macrophages in Atherosclerosis. Front Cardiovasc Med 2022; 9:868788. [PMID: 35425818 PMCID: PMC9001883 DOI: 10.3389/fcvm.2022.868788] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/04/2022] [Indexed: 02/05/2023] Open
Abstract
Emerging research on epigenetics has resulted in many novel discoveries in atherosclerosis (AS), an inflammaging-associated disease characterized by chronic inflammation primarily driven by macrophages. The bulk of evidence has demonstrated the central role of epigenetic machinery in macrophage polarization to pro- (M1-like) or anti-inflammatory (M2-like) phenotype. An increasing number of epigenetic alterations and their modifiers involved in reprogramming macrophages by regulating DNA methylation or histone modifications (e.g., methylation, acetylation, and recently lactylation) have been identified. They may act to determine or skew the direction of macrophage polarization in AS lesions, thereby representing a promising target. Here we describe the current understanding of the epigenetic machinery involving macrophage polarization, to shed light on chronic inflammation-driving onset and progression of inflammaging-associated diseases, using AS as a prototypic example, and discuss the challenge for developing effective therapies targeting the epigenetic modifiers against these diseases, particularly highlighting a potential strategy based on epigenetically-governed repolarization from M1-like to M2-like phenotype.
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Affiliation(s)
- Hongmei Yang
- Laboratory of Cancer Precision Medicine, The First Hospital of Jilin University, Changchun, China.,Department of Critical Care Medicine, The First Hospital of Jilin University, Changchun, China
| | - Yue Sun
- Laboratory of Cancer Precision Medicine, The First Hospital of Jilin University, Changchun, China
| | - Qingchao Li
- Laboratory of Cancer Precision Medicine, The First Hospital of Jilin University, Changchun, China
| | - Fengyan Jin
- Department of Hematology, The First Hospital of Jilin University, Changchun, China
| | - Yun Dai
- Laboratory of Cancer Precision Medicine, The First Hospital of Jilin University, Changchun, China
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42
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Joshi S, Paul P, Hartman JM, Perry SE. AGL15 Promotion of Somatic Embryogenesis: Role and Molecular Mechanism. FRONTIERS IN PLANT SCIENCE 2022; 13:861556. [PMID: 35419012 PMCID: PMC8996056 DOI: 10.3389/fpls.2022.861556] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/01/2022] [Indexed: 06/14/2023]
Abstract
Plants have amazing regenerative properties with single somatic cells, or groups of cells able to give rise to fully formed plants. One means of regeneration is somatic embryogenesis, by which an embryonic structure is formed that "converts" into a plantlet. Somatic embryogenesis has been used as a model for zygotic processes that are buried within layers of maternal tissues. Understanding mechanisms of somatic embryo induction and development are important as a more accessible model for seed development. We rely on seed development not only for most of our caloric intake, but also as a delivery system for engineered crops to meet agricultural challenges. Regeneration of transformed cells is needed for this applied work as well as basic research to understand gene function. Here we focus on a MADS-domain transcription factor, AGAMOUS-Like15 (AGL15) that shows a positive correlation between accumulation levels and capacity for somatic embryogenesis. We relate AGL15 function to other transcription factors, hormones, and epigenetic modifiers involved in somatic embryo development.
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Affiliation(s)
- Sanjay Joshi
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
| | - Priyanka Paul
- Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, United States
| | - Jeanne M. Hartman
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
| | - Sharyn E. Perry
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
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43
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Huerne K, Palmour N, Wu AR, Beck S, Berner A, Siebert R, Joly Y. Auditing the Editor: A Review of Key Translational Issues in Epigenetic Editing. CRISPR J 2022; 5:203-212. [PMID: 35325565 DOI: 10.1089/crispr.2021.0094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Currently, most advances in site-specific epigenetic editing for human use are concentrated in basic research, yet, there is considerable interest to translate this technology beyond the bench. This review highlights recent developments with epigenetic editing technology in comparison with the canonical CRISPR-Cas genome editing, as well as the epistemic and ethical considerations with preemptive translation of epigenetic editing into clinical or commercial use in humans. Key considerations in safety, equity, and access to epigenetic editing are highlighted, with a spotlight on the ethical, legal, and social issues of this technology in the context of global health equity.
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Affiliation(s)
- Katherine Huerne
- Centre of Genomics and Policy, McGill University, Montreal, Canada
| | - Nicole Palmour
- Centre of Genomics and Policy, McGill University, Montreal, Canada
| | - Angela Ruohao Wu
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong S.A.R, China.,Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong S.A.R, China
| | - Stephan Beck
- University College London (UCL) Cancer Institute, London, United Kingdom
| | - Alison Berner
- Barts Cancer Institute, Queen Mary University of London (QMUL), London, United Kingdom
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Yann Joly
- Centre of Genomics and Policy, McGill University, Montreal, Canada
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44
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Comprehensive 3D epigenomic maps define limbal stem/progenitor cell function and identity. Nat Commun 2022; 13:1293. [PMID: 35277509 PMCID: PMC8917218 DOI: 10.1038/s41467-022-28966-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/21/2022] [Indexed: 11/24/2022] Open
Abstract
The insights into how genome topology couples with epigenetic states to govern the function and identity of the corneal epithelium are poorly understood. Here, we generate a high-resolution Hi-C interaction map of human limbal stem/progenitor cells (LSCs) and show that chromatin multi-hierarchical organisation is coupled to gene expression. By integrating Hi-C, epigenome and transcriptome data, we characterize the comprehensive 3D epigenomic landscapes of LSCs. We find that super-silencers mediate gene repression associated with corneal development, differentiation and disease via chromatin looping and/or proximity. Super-enhancer (SE) interaction analysis identified a set of SE interactive hubs that contribute to LSC-specific gene activation. These active and inactive element-anchored loop networks occur within the cohesin-occupied CTCF-CTCF loops. We further reveal a coordinated regulatory network of core transcription factors based on SE-promoter interactions. Our results provide detailed insights into the genome organization principle for epigenetic regulation of gene expression in stratified epithelia. Genome topology provides a structural basis for epigenome-mediated transcriptional regulation in eukaryotes. Here the authors characterized the 3D genome of stratified squamous epithelia. They generated a Hi-C map of human limbal stem/progenitor cells (LSCs) and integrated these data with epigenomics, transcription factor binding maps, and transcriptome data.
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DNA Hypomethylation Is Associated with the Overexpression of INHBA in Upper Tract Urothelial Carcinoma. Int J Mol Sci 2022; 23:ijms23042072. [PMID: 35216189 PMCID: PMC8877459 DOI: 10.3390/ijms23042072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/20/2022] [Accepted: 01/24/2022] [Indexed: 02/04/2023] Open
Abstract
Urothelial carcinoma includes upper urinary tract cancer (UTUC) and bladder cancer. Although nephroureterectomy is the standard treatment for UTUC, the recurrence rate is approximately half and the tumor is associated with poor prognoses. Metastases are the most devastating and lethal clinical situation in urothelial carcinoma. Despite its clinical importance, few potential diagnostic biomarkers are suitable for early UC detection. We compared high-stage/high-grade urothelial carcinoma tissues to adjacent normal urothelial tissues using methyl-CpG binding domain protein capture for genome-wide DNA methylation analysis. Based on our findings, inhibin βA (INHBA) might be associated with carcinogenesis and metastasis. Further, clinical UC specimens had significant INHBA hypomethylation based on pyrosequencing. INHBA was detected by real-time PCR and immunohistochemistry staining, and was found to be highly expressed in clinical tissues and cell lines of urothelial carcinoma. Further, INHBA depletion was found to significantly reduce BFTC-909 cell growth and migration by INHBA-specific small interfering RNA. Interestingly, a positive correlation was found between SMAD binding and extracellular structure organization with INHBA using gene set enrichment analysis and gene ontology analysis. Together, these results are the first evidence of INHBA promoter hypomethylation and INHBA overexpression in UTUC. INHBA may affect urothelial carcinoma migration by reorganizing the extracellular matrix through the SMAD pathway.
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Tanemoto F, Mimura I. Therapies Targeting Epigenetic Alterations in Acute Kidney Injury-to-Chronic Kidney Disease Transition. Pharmaceuticals (Basel) 2022; 15:ph15020123. [PMID: 35215236 PMCID: PMC8877070 DOI: 10.3390/ph15020123] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/15/2022] [Accepted: 01/18/2022] [Indexed: 12/04/2022] Open
Abstract
Acute kidney injury (AKI) was previously thought to be a merely transient event; however, recent epidemiological evidence supports the existence of a causal relationship between AKI episodes and subsequent progression to chronic kidney disease (CKD). Although the pathophysiology of this AKI-to-CKD transition is not fully understood, it is mediated by the interplay among multiple components of the kidney including tubular epithelial cells, endothelial cells, pericytes, inflammatory cells, and myofibroblasts. Epigenetic alterations including histone modification, DNA methylation, non-coding RNAs, and chromatin conformational changes, are also expected to be largely involved in the pathophysiology as a “memory” of the initial injury that can persist and predispose to chronic progression of fibrosis. Each epigenetic modification has a great potential as a therapeutic target of AKI-to-CKD transition; timely and target-specific epigenetic interventions to the various temporal stages of AKI-to-CKD transition will be the key to future therapeutic applications in clinical practice. This review elaborates on the latest knowledge of each mechanism and the currently available therapeutic agents that target epigenetic modification in the context of AKI-to-CKD transition. Further studies will elucidate more detailed mechanisms and novel therapeutic targets of AKI-to-CKD transition.
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Chakravarti R, Lenka SK, Gautam A, Singh R, Ravichandiran V, Roy S, Ghosh D. A Review on CRISPR-Mediated Epigenome Editing: A Future Directive for Therapeutic Management of Cancer. Curr Drug Targets 2022; 23:836-853. [DOI: 10.2174/1389450123666220117105531] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/15/2021] [Accepted: 12/14/2021] [Indexed: 11/22/2022]
Abstract
Abstract:
Recent studies have shed light on the role of epigenetic marks in certain diseases like cancer, type II diabetes mellitus (T2DM), obesity, and cardiovascular dysfunction, to name a few. Epigenetic marks like DNA methylation and histone acetylation are randomly altered in the disease state. It has been seen that methylation of DNA and histones can result in down-regulation of gene expression, whereas histone acetylation, ubiquitination, and phosphorylation are linked to enhanced expression of genes. How can we precisely target such epigenetic aberrations to prevent the advent of diseases? The answer lies in the amalgamation of the efficient genome editing technique, CRISPR, with certain effector molecules that can alter the status of epigenetic marks as well as employ certain transcriptional activators or repressors. In this review, we have discussed the rationale of epigenetic editing as a therapeutic strategy and how CRISPR-Cas9 technology coupled with epigenetic effector tags can efficiently edit epigenetic targets. In the later part, we have discussed how certain epigenetic effectors are tagged with dCas9 to elicit epigenetic changes in cancer. Increased interest in exploring the epigenetic background of cancer and non-communicable diseases like type II diabetes mellitus and obesity accompanied with technological breakthroughs has made it possible to perform large-scale epigenome studies.
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Affiliation(s)
- Rudra Chakravarti
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Swadhin Kumar Lenka
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Anupam Gautam
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany
| | - Rajveer Singh
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Velayutham Ravichandiran
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Syamal Roy
- CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata, India
| | - Dipanjan Ghosh
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
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Williams LA, LaSalle JM. Future Prospects for Epigenetics in Autism Spectrum Disorder. Mol Diagn Ther 2022; 26:569-579. [PMID: 35962910 PMCID: PMC9626414 DOI: 10.1007/s40291-022-00608-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2022] [Indexed: 12/30/2022]
Abstract
Despite decades of investigation into the genetics of autism spectrum disorder (ASD), a current consensus in the field persists that ASD risk is too heterogeneous to be diagnosed by a single set of genetic variants. As such, ASD research has broadened to include assessment of other molecular biomarkers implicated in the condition that may be reflective of environmental exposures or gene by environment interactions. Epigenetic variance, and specifically differential DNA methylation, have emerged as areas of particularly high interest to ASD, as the epigenetic markers from specific chromatin loci collectively can reflect influences of multiple genetic and environmental factors and can also result in differential gene expression patterns. This review examines recent studies of the ASD epigenome, detailing common gene pathways found to be differentially methylated in people with ASD, and considers how these discoveries may inform our understanding of ASD etiology. We also consider future applications of epigenetics in ASD research and clinical practice, focusing on substratification, biomarker development, and experimental preclinical models of ASD that test causality. In combination with other -omics approaches, epigenomics allows an improved conceptualization of the multifactorial nature of ASD, and opens future lines of inquiry for both basic research and clinical practice.
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Affiliation(s)
- Logan A. Williams
- grid.27860.3b0000 0004 1936 9684Department of Medical Microbiology and Immunology, University of California Davis School of Medicine, Davis, CA USA ,grid.27860.3b0000 0004 1936 9684Perinatal Origins of Disparities Center, University of California Davis, Davis, CA USA ,grid.27860.3b0000 0004 1936 9684MIND Institute, University of California Davis, Davis, CA USA ,grid.27860.3b0000 0004 1936 9684Genome Center, University of California Davis, Davis, CA USA
| | - Janine M. LaSalle
- grid.27860.3b0000 0004 1936 9684Department of Medical Microbiology and Immunology, University of California Davis School of Medicine, Davis, CA USA ,grid.27860.3b0000 0004 1936 9684Perinatal Origins of Disparities Center, University of California Davis, Davis, CA USA ,grid.27860.3b0000 0004 1936 9684MIND Institute, University of California Davis, Davis, CA USA ,grid.27860.3b0000 0004 1936 9684Genome Center, University of California Davis, Davis, CA USA
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At the dawn: cell-free DNA fragmentomics and gene regulation. Br J Cancer 2021; 126:379-390. [PMID: 34815523 PMCID: PMC8810841 DOI: 10.1038/s41416-021-01635-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 11/03/2021] [Accepted: 11/09/2021] [Indexed: 12/14/2022] Open
Abstract
Epigenetic mechanisms play instrumental roles in gene regulation during embryonic development and disease progression. However, it is challenging to non-invasively monitor the dynamics of epigenomes and related gene regulation at inaccessible human tissues, such as tumours, fetuses and transplanted organs. Circulating cell-free DNA (cfDNA) in peripheral blood provides a promising opportunity to non-invasively monitor the genomes from these inaccessible tissues. The fragmentation patterns of plasma cfDNA are unevenly distributed in the genome and reflect the in vivo gene-regulation status across multiple molecular layers, such as nucleosome positioning and gene expression. In this review, we revisited the computational and experimental approaches that have been recently developed to measure the cfDNA fragmentomics across different resolutions comprehensively. Moreover, cfDNA in peripheral blood is released following cell death, after apoptosis or necrosis, mainly from haematopoietic cells in healthy people and diseased tissues in patients. Several cfDNA-fragmentomics approaches showed the potential to identify the tissues-of-origin in cfDNA from cancer patients and healthy individuals. Overall, these studies paved the road for cfDNA fragmentomics to non-invasively monitor the in vivo gene-regulatory dynamics in both peripheral immune cells and diseased tissues.
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Kitsou K, Iliopoulou M, Spoulou V, Lagiou P, Magiorkinis G. Viral Causality of Human Cancer and Potential Roles of Human Endogenous Retroviruses in the Multi-Omics Era: An Evolutionary Epidemiology Review. Front Oncol 2021; 11:687631. [PMID: 34778024 PMCID: PMC8586426 DOI: 10.3389/fonc.2021.687631] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 10/12/2021] [Indexed: 12/20/2022] Open
Abstract
Being responsible for almost 12% of cancers worldwide, viruses are among the oldest known and most prevalent oncogenic agents. The quality of the evidence for the in vivo tumorigenic potential of microorganisms varies, thus accordingly, viruses were classified in 4 evidence-based categories by the International Agency for Research on Cancer in 2009. Since then, our understanding of the role of viruses in cancer has significantly improved, firstly due to the emergence of high throughput sequencing technologies that allowed the “brute-force” recovery of unknown viral genomes. At the same time, multi-omics approaches unravelled novel virus-host interactions in stem-cell biology. We now know that viral elements, either exogenous or endogenous, have multiple sometimes conflicting roles in human pathophysiology and the development of cancer. Here we integrate emerging evidence on viral causality in human cancer from basic mechanisms to clinical studies. We analyze viral tumorigenesis under the scope of deep-in-time human-virus evolutionary relationships and critically comment on the evidence through the eyes of clinical epidemiology, firstly by reviewing recognized oncoviruses and their mechanisms of inducing tumorigenesis, and then by examining the potential role of integrated viruses in our genome in the process of carcinogenesis.
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Affiliation(s)
- Konstantina Kitsou
- Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece.,Immunobiology and Vaccinology Research Laboratory, First Department of Peadiatrics, "Aghia Sophia" Children's Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria Iliopoulou
- Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Vana Spoulou
- Immunobiology and Vaccinology Research Laboratory, First Department of Peadiatrics, "Aghia Sophia" Children's Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Pagona Lagiou
- Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Gkikas Magiorkinis
- Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
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